Cd45, Cd11b, Cx3cr1 will work. Even Cd45/Cd11b alone will be sufficient. Check out the protocol in this paper in which they extracted microglia from as young as E14.5 :Article Single-Cell RNA Sequencing of Microglia throughout the Mouse...
I have used these markers consistently for the past two years, and they work great!
I would also recommend this paper for a protocol (attached). If you need the cells in good health - stick with the cell surface markers. IBA1 is beautiful, but it requires permeabilization of the cells, so you could count them, but do limited molecular biology afterwards.